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- PDB-9f21: Crystal structure of Borrelia burgdorferi CspZ-YACS -

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Basic information

Entry
Database: PDB / ID: 9f21
TitleCrystal structure of Borrelia burgdorferi CspZ-YACS
ComponentsComplement regulator-acquiring surface protein 2 (CRASP-2)
KeywordsIMMUNE SYSTEM / complement-binding protein / Lyme disease / borreliosis.
Function / homology: / Complement regulator-acquiring surface protein 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / metal ion binding / Complement regulator-acquiring surface protein 2 (CRASP-2)
Function and homology information
Biological speciesBorreliella burgdorferi B31 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsBrangulis, K. / Malfetano, J. / Marcinkiewicz, A.L. / Wang, A. / Chen, Y.-L. / Yang, X. / Lee, W. / Bottazzi, M.-E. / Pal, U. / Hsieh, C.-L. ...Brangulis, K. / Malfetano, J. / Marcinkiewicz, A.L. / Wang, A. / Chen, Y.-L. / Yang, X. / Lee, W. / Bottazzi, M.-E. / Pal, U. / Hsieh, C.-L. / Chen, W.-H. / Lin, Y.-P.
Funding support1items
OrganizationGrant numberCountry
Other governmentlzp-2021/1-0068
CitationJournal: Nat Commun / Year: 2025
Title: Mechanistic insights into the structure-based design of a CspZ-targeting Lyme disease vaccine.
Authors: Brangulis, K. / Malfetano, J. / Marcinkiewicz, A.L. / Wang, A. / Chen, Y.L. / Lee, J. / Liu, Z. / Yang, X. / Strych, U. / Tupina, D. / Akopjana, I. / Bottazzi, M.E. / Pal, U. / Hsieh, C.L. / ...Authors: Brangulis, K. / Malfetano, J. / Marcinkiewicz, A.L. / Wang, A. / Chen, Y.L. / Lee, J. / Liu, Z. / Yang, X. / Strych, U. / Tupina, D. / Akopjana, I. / Bottazzi, M.E. / Pal, U. / Hsieh, C.L. / Chen, W.H. / Lin, Y.P.
History
DepositionApr 20, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Complement regulator-acquiring surface protein 2 (CRASP-2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3463
Polymers25,1541
Non-polymers1922
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-12 kcal/mol
Surface area11580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.551, 41.677, 162.812
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Complement regulator-acquiring surface protein 2 (CRASP-2)


Mass: 25153.645 Da / Num. of mol.: 1 / Mutation: Tyr207Ala; Tyr211Ala; Cys187Ser
Source method: isolated from a genetically manipulated source
Details: The first 4 residues (GAMG) are remnants from the expression tag. There are three mutations introduced - Tyr207Ala, Tyr211Ala and Cys187Ser.
Source: (gene. exp.) Borreliella burgdorferi B31 (bacteria) / Gene: cspZ, BB_H06 / Plasmid: pETm-11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O50665
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.64 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 2.2 M ammonium sulfate 0.1 M HEPES 7.5 2% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.95→41.68 Å / Num. obs: 16483 / % possible obs: 99.9 % / Redundancy: 12.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.095 / Net I/σ(I): 18.1
Reflection shellResolution: 1.95→2 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.693 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 1144 / CC1/2: 0.971 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→40.74 Å / Cor.coef. Fo:Fc: 0.884 / Cor.coef. Fo:Fc free: 0.867 / SU B: 5.299 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.24 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2551 839 5.3 %RANDOM
Rwork0.23047 ---
obs0.2318 14928 95.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.034 Å2
Baniso -1Baniso -2Baniso -3
1-4.51 Å20 Å20 Å2
2---1.2 Å20 Å2
3----3.3 Å2
Refinement stepCycle: 1 / Resolution: 1.95→40.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1738 0 10 179 1927
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131769
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161716
X-RAY DIFFRACTIONr_angle_refined_deg1.5711.6332373
X-RAY DIFFRACTIONr_angle_other_deg1.4121.5953961
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.175216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.90424.51693
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.95915347
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.961157
X-RAY DIFFRACTIONr_chiral_restr0.0840.2235
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021981
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02393
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9162.922867
X-RAY DIFFRACTIONr_mcbond_other2.9032.922866
X-RAY DIFFRACTIONr_mcangle_it4.5894.3721082
X-RAY DIFFRACTIONr_mcangle_other4.5874.3721083
X-RAY DIFFRACTIONr_scbond_it3.5933.361902
X-RAY DIFFRACTIONr_scbond_other3.5443.306895
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5544.7831280
X-RAY DIFFRACTIONr_long_range_B_refined8.5335.5912111
X-RAY DIFFRACTIONr_long_range_B_other8.42635.362087
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 59 -
Rwork0.318 1032 -
obs--91.45 %

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